Pôle Scientifique de Modélisation Numérique (PSMN)
All nf-core pipelines have been successfully configured for use on the tars cluster at the Institut Pasteur.
To use, run the pipeline with -profile pasteur. This will download and launch the psmn.config which has been pre-configured with a setup suitable for the PSMN cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Running the workflow on the PSMN cluster
Install Nextflow and Charliecloud
The Nextflow binary is available in the folder /Xnfs/abc/nextflow_bin/.
All the Charliecloud binaries are available in the folder Xnfs/abc/charliecloud_bin/.
You can update your $PATH variable with the following command to have access to Nextflow and Charliecloud:
PATH=/Xnfs/abc/charliecloud_bin/:/Xnfs/abc/nextflow_bin/:$PATHPATH=/Xnfs/abc/charliecloud_bin/:/Xnfs/abc/nextflow_bin/:$PATHor add this line to your ~/.zshrc or ~/.bashrc configuration file.
Install nf-core
nf-core is available on the PSMN as a Charliecloud container you can run the classical nf-core command by prefixing them with:
ch-run -b /scratch:/scratch /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-corech-run -b /scratch:/scratch /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-coreFor exemple to download the nf-core/rnaseq pipeline you can use the command:
ch-run -b /scratch:/scratch \
/Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
download rnaseq -r 3.9 --outdir nf-core-rnaseqch-run -b /scratch:/scratch \
/Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
download rnaseq -r 3.9 --outdir nf-core-rnaseqDownload and launch a nf-core pipeline
You can use the nf-core download command to download an nf-core pipeline and the configuration files for the PSMN:
cd <your scratch directory>
ch-run -b /scratch:/scratch \
/Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
download rnaseq -r 3.9 --outdir <your scratch directory>/nf-core-rnaseq -x none -c none
The you can launch this pipeline with the PSMN profile
tmux
cd nf-core-rnaseq
nextflow run workflow -profile test,psmn --outdir results/
Config file
//Profile config names for nf-core/configs
params {
config_profile_description = 'PSMN (Pôle Scientifique de Modélisation Numérique) HPC cluster profile'
config_profile_contact = 'Laurent Modolo (@l-modolo)'
config_profile_url = 'http://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil'
}
charliecloud {
enabled = true
cacheDir = "/Xnfs/abc/charliecloud"
runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
readOnlyInputs = true
}
process {
executor = 'slurm'
clusterOptions = "--partition=Lake"
}
params {
max_memory = 512.GB
max_cpus = 32
max_time = 24.h
}
//Profile config names for nf-core/configs
params {
config_profile_description = 'PSMN (Pôle Scientifique de Modélisation Numérique) HPC cluster profile'
config_profile_contact = 'Laurent Modolo (@l-modolo)'
config_profile_url = 'http://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil'
}
charliecloud {
enabled = true
cacheDir = "/Xnfs/abc/charliecloud"
runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
readOnlyInputs = true
}
process {
executor = 'slurm'
clusterOptions = "--partition=Lake"
}
params {
max_memory = 512.GB
max_cpus = 32
max_time = 24.h
}
executor
contact
